Plant Circular RNA Database

Detail information of Solyc09g055350.2_circ_g.3

			
						 General Information
					
						CircRNA Name
						Solyc09g055350.2_circ_g.3
					
						ID in PlantcircBase
						sly_circ_002868
					
						Alias
						NA
					
						Organism
						
							Solanum lycopersicum						
					
						Position
						
							chr9: 40045439-40048634  JBrowse»						
					
						Reference genome
						
							SL2.50.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Solyc09g055350.2						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Solyc09g055350.2_circ_g.1 Solyc09g055350.2_circ_g.2 Solyc09g055350.2_circ_g.4 						
					
						Support reads
						14
					
						Tissues
						fruit
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							GT-AG							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Solyc09g055350.2.1:6

General Information
CircRNA Name	Solyc09g055350.2_circ_g.3
ID in PlantcircBase	sly_circ_002868
Alias	NA
Organism	Solanum lycopersicum
Position	chr9: 40045439-40048634 JBrowse»
Reference genome	SL2.50.38
Type	e-circRNA
Identification method	CIRI
Parent gene	Solyc09g055350.2
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Solyc09g055350.2_circ_g.1 Solyc09g055350.2_circ_g.2 Solyc09g055350.2_circ_g.4
Support reads	14
Tissues	fruit
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	GT-AG The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Solyc09g055350.2.1:6

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							GCTGTTCCAGCTATCGCTTCCACTGAATTTCCTTGGTAGCGTATATCGTGAGACCATCCAAAGT
TTAGTGGACATGAAATCAATGTTTCAGTTACTAGAGtcgagaaacaggtggtcttaatcgggtc
attgaccgtggtagccgagctatcaattttattctttcgtcaatggttttcaatgttttcccga
cgatattg

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 619
Transcript exons: 40045439-40045541,40045654-40045761,40045956-40046039,40
046155-40046215,40048283-40048428,40048518-40048634
TCGAGAAACAGGTGGTCTTAATCGGGTCATTGACCGTGGTAGCCGAGCTATCAATTTTATTCTT
TCGTCAATGGTTTTCAATGTTTTCCCGACGATATTGGAGATATCAATGGTATCAGGTATACTTG
CATACAGATTTGGAGCTTCCTTTGCATGGATTACATCACTGTCAGTGGCTGCATATATCGCTTT
CACCTTAAGTATTACCCAGTGGCGAACTAAGTTTAGGAAGGAGATGAATAAAGCTGATAATGAT
GCAAGCACACGAGCAATCGATTCTCTTATCAACTATGAGACTGTTAAGTACTTTAACAATGAGG
TGTATGAAACCGAGAAGTATGATCACTTTTTAAAGAGATATGAAGATGCTGCCTTAAAGACACA
ACGTAGTCTTGCAATCTTAAACTTTGGGCAAAGTGCAATATTCAGCATAGCTCTCTCAGCTGCT
ATGGTTTTATGTTCTAATGGGATTATGAATGGTGTCATGACTGTTGGTGACTTGGTCATGGTAA
ACGGGCTGCTGTTCCAGCTATCGCTTCCACTGAATTTCCTTGGTAGCGTATATCGTGAGACCAT
CCAAAGTTTAGTGGACATGAAATCAATGTTTCAGTTACTAGAG
						
					

						Genomic sequence
						
							TCGAGAAACAGGTGGTCTTAATCGGGTCATTGACCGTGGTAGCCGAGCTATCAATTTTATTCTT
TCGTCAATGGTTTTCAATGTTTTCCCGACGATATTGGAGGTATATATCATTTATTCCATCATTT
AGAAGGCAGCATTTCTGATTAAAAATTCCTAAATTTCTCATGTTGCTTCAAGTATTACTCCAAC
TGTATTAACATGAACCTTTTCAGATATCAATGGTATCAGGTATACTTGCATACAGATTTGGAGC
TTCCTTTGCATGGATTACATCACTGTCAGTGGCTGCATATATCGCTTTCACCTTAAGTATTACC
CAGGTTATCTACGAGCTAAACTCATCAAGTATTAGGAAAGGTCTTCTATTTTTGGATTTCATGT
CCCTTTCCATCTTTTAGTTATTTATGGTCATACTAGTGGCAGTTAGGTGATAGCTGATATATCA
GTAACTTTTAGTGAGTCTGGCTTCTAGTATCTTTTGTCCAAAACTTCCTGTTCATTTTGTATCT
TACAGTGGCGAACTAAGTTTAGGAAGGAGATGAATAAAGCTGATAATGATGCAAGCACACGAGC
AATCGATTCTCTTATCAACTATGAGGTAAGCTTGTGTTTCTACGTACCATGGTTAACTTGTTTT
ACCATGATTAACTTATTTTATCCATTTTCTGATATGCAATACACTTGATTGTATTGGCAATTTT
CATTTTTGACAGACTGTTAAGTACTTTAACAATGAGGTGTATGAAACCGAGAAGTATGATCACT
TTTTAAAGAGTAAGTTGTAATACCTTATGGCTTTTCCCTATCATATAATAAGCTCTTCTGCACT
CTTATGTTATGTTATTATGTTTTGTATATGTTGGGTGAATCAGATTGCATCAACTGTGCTAACA
TTTATGATTTAACACAGTTTTTGGCAATTAGTTTAAGTCCAAATTTCAGGTAAAGTATAGGAGA
AGTTCAATCTTATCATGATTTAAGTTACTTGATAAAGAAAAACATAAATCATTGAAATTTATTC
AGTTTCACAGAATGGATACCTTGTCTACATGGCTTCCCTTCAACAAACATGGGTTGGCTTCACC
TTATCAGAAAAATAGAAACATGGGTTTGCTTCACTGTAAGTGTACACTTTGTTGTGGAATCTAG
CGATAAAGCAAAACAGAAGAATATGTTCTTTTTCCTTTGTGGTCTTAAAACTATTATATACTAG
TGTACTAAAGGAACTGATCATATACTTTCTGTGCAATATGAGAATTATTGGATGGTCAGTCAAG
TTGAGCGATAGAGGCTACTTGGGAGATGTTTGCTTACTTGCCCGATTTGGAATAAACTCATTAT
ATTACTTTAGAGCAATAGGATCATGACTGGGTGGTGGACCATGCAAAACTTATGTCATGACTGT
ATCCAAGCTTATGACAATAACTACCATCGGGTCTAGGTTTCCAAAAACTACCTCCTCGTGGATT
CTCCATAGATTGATATGTTCGCTTTTCTATGAATTGAGATGCGAGAACAAAGGAGACATTGGTC
GGTGATAAAACTACTTTGTGACTTGGCAGTGCGGCACGACGAAGTAGACGAGAGAATAATTCAT
TAACTGTAGGAGCGCTAGGACTAGCTAAAATCTAAACACACTGAATGATGGTAAGTAGGAAATC
CAATGCGTGGTCAGATCTTGCTGGAAAAGTCGCACGTTAGGTTTTTGTTGCTGGAGAGTGGGGG
ACCCATGGTGGTGTTGGTTTTCTCACATTATTGATAAAAACAGCTGATGATGCAAATCAGCCCC
AACAGTCGCCAGAAGTTGATGCACGATGACTTGTTGACTGAGTTTTCTTCCCCGTATTTCTCAC
CAATGCTCTACTACCATGTGAAAAATATTGGAGAAGAATATTATTGAATTGTGTATTTACATTA
TTATACAAAGACTACTTATAATCATTATTATACAATCCTTCATAAAAAAATAATACAATTCTTT
ATCAAGTAGGATTCTATATACTATTCCCATTCTAAGTAGGATTGTATATGCTATTCTTCTTCCT
ATCTTATTCTAACACTACCAAAACACCATCAAACACCAAATCTATATCTGGTAAATCAGCCATG
AACGCCCATCACCTTCACAGTACATCCGATTCTATGACAGCTGGAAACAACCATTTCTCTGACC
AATTCATCTTTTTCTATGACACCCTGATATTACACTCCCTCTAGCCTATCTAACAATCATAGCC
TCCCTCAAAGATTAGTTTATCCGGTTGAAATTGTGTCTGATTCGCCCGTTGAAACTCCAGTTTG
AGGTGACGGTGATGTTCGAAGTAGCATTGCAGTCAAATTTTCCAGAATTTTCCTGCTTTATTCT
TATTGAAAGGGCCAATTTTCTTATTCTTGCTTGTGATGGGGACATGGGGTATGTATCCAGCTTG
CAGTCTTCGAAGCAGCGAGATTTTAGTGCGTAAGGTTTGTATAGAATTTAGGAAGACATTTCTT
CTGTGATATTTATTTTAGTGTATATTTAATAATTAAATTATTGTGTGGAAGTTCTCAAGAACCT
GGAAAAATAGATACCTGATCATTGAAGCATGCCCCATCACGTGGTTGAGGATCCTCAATTATAA
AGATATATATAATTAAATTATTGTGTGAAAGTTTCCAAGAACCTGGAAAAAAATAGATAACTGG
TCATTGCAGCATGCCACATCACCGGGTTGAGGATCTTCAGTTATATAGATATATAGACATAGAT
TCATTGGCTTATGATATACAAAACTTTGACTGTTACGTTGTCCTCATTTTCTTTTATTGGAATA
AGCAATCATGATATTATGTTGTCTCCAGGATATGAAGATGCTGCCTTAAAGACACAACGTAGTC
TTGCAATCTTAAACTTTGGGCAAAGTGCAATATTCAGCATAGCTCTCTCAGCTGCTATGGTTTT
ATGTTCTAATGGGATTATGAATGGTGTCATGACTGTTGGTGACTTGGTAGAACTTTTTCTCTAA
TTACCTTAGCTGAGTGATTATTTTTTCTGCAGTGTTAGCCCTCTAATAAGAAATATTACTATTT
TTTATAGGTCATGGTAAACGGGCTGCTGTTCCAGCTATCGCTTCCACTGAATTTCCTTGGTAGC
GTATATCGTGAGACCATCCAAAGTTTAGTGGACATGAAATCAATGTTTCAGTTACTAGAG
						
					

			
		

Sequences
Splice junction sequence	GCTGTTCCAGCTATCGCTTCCACTGAATTTCCTTGGTAGCGTATATCGTGAGACCATCCAAAGT TTAGTGGACATGAAATCAATGTTTCAGTTACTAGAGtcgagaaacaggtggtcttaatcgggtc attgaccgtggtagccgagctatcaattttattctttcgtcaatggttttcaatgttttcccga cgatattg
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 619 Transcript exons: 40045439-40045541,40045654-40045761,40045956-40046039,40 046155-40046215,40048283-40048428,40048518-40048634 TCGAGAAACAGGTGGTCTTAATCGGGTCATTGACCGTGGTAGCCGAGCTATCAATTTTATTCTT TCGTCAATGGTTTTCAATGTTTTCCCGACGATATTGGAGATATCAATGGTATCAGGTATACTTG CATACAGATTTGGAGCTTCCTTTGCATGGATTACATCACTGTCAGTGGCTGCATATATCGCTTT CACCTTAAGTATTACCCAGTGGCGAACTAAGTTTAGGAAGGAGATGAATAAAGCTGATAATGAT GCAAGCACACGAGCAATCGATTCTCTTATCAACTATGAGACTGTTAAGTACTTTAACAATGAGG TGTATGAAACCGAGAAGTATGATCACTTTTTAAAGAGATATGAAGATGCTGCCTTAAAGACACA ACGTAGTCTTGCAATCTTAAACTTTGGGCAAAGTGCAATATTCAGCATAGCTCTCTCAGCTGCT ATGGTTTTATGTTCTAATGGGATTATGAATGGTGTCATGACTGTTGGTGACTTGGTCATGGTAA ACGGGCTGCTGTTCCAGCTATCGCTTCCACTGAATTTCCTTGGTAGCGTATATCGTGAGACCAT CCAAAGTTTAGTGGACATGAAATCAATGTTTCAGTTACTAGAG
Genomic sequence	TCGAGAAACAGGTGGTCTTAATCGGGTCATTGACCGTGGTAGCCGAGCTATCAATTTTATTCTT TCGTCAATGGTTTTCAATGTTTTCCCGACGATATTGGAGGTATATATCATTTATTCCATCATTT AGAAGGCAGCATTTCTGATTAAAAATTCCTAAATTTCTCATGTTGCTTCAAGTATTACTCCAAC TGTATTAACATGAACCTTTTCAGATATCAATGGTATCAGGTATACTTGCATACAGATTTGGAGC TTCCTTTGCATGGATTACATCACTGTCAGTGGCTGCATATATCGCTTTCACCTTAAGTATTACC CAGGTTATCTACGAGCTAAACTCATCAAGTATTAGGAAAGGTCTTCTATTTTTGGATTTCATGT CCCTTTCCATCTTTTAGTTATTTATGGTCATACTAGTGGCAGTTAGGTGATAGCTGATATATCA GTAACTTTTAGTGAGTCTGGCTTCTAGTATCTTTTGTCCAAAACTTCCTGTTCATTTTGTATCT TACAGTGGCGAACTAAGTTTAGGAAGGAGATGAATAAAGCTGATAATGATGCAAGCACACGAGC AATCGATTCTCTTATCAACTATGAGGTAAGCTTGTGTTTCTACGTACCATGGTTAACTTGTTTT ACCATGATTAACTTATTTTATCCATTTTCTGATATGCAATACACTTGATTGTATTGGCAATTTT CATTTTTGACAGACTGTTAAGTACTTTAACAATGAGGTGTATGAAACCGAGAAGTATGATCACT TTTTAAAGAGTAAGTTGTAATACCTTATGGCTTTTCCCTATCATATAATAAGCTCTTCTGCACT CTTATGTTATGTTATTATGTTTTGTATATGTTGGGTGAATCAGATTGCATCAACTGTGCTAACA TTTATGATTTAACACAGTTTTTGGCAATTAGTTTAAGTCCAAATTTCAGGTAAAGTATAGGAGA AGTTCAATCTTATCATGATTTAAGTTACTTGATAAAGAAAAACATAAATCATTGAAATTTATTC AGTTTCACAGAATGGATACCTTGTCTACATGGCTTCCCTTCAACAAACATGGGTTGGCTTCACC TTATCAGAAAAATAGAAACATGGGTTTGCTTCACTGTAAGTGTACACTTTGTTGTGGAATCTAG CGATAAAGCAAAACAGAAGAATATGTTCTTTTTCCTTTGTGGTCTTAAAACTATTATATACTAG TGTACTAAAGGAACTGATCATATACTTTCTGTGCAATATGAGAATTATTGGATGGTCAGTCAAG TTGAGCGATAGAGGCTACTTGGGAGATGTTTGCTTACTTGCCCGATTTGGAATAAACTCATTAT ATTACTTTAGAGCAATAGGATCATGACTGGGTGGTGGACCATGCAAAACTTATGTCATGACTGT ATCCAAGCTTATGACAATAACTACCATCGGGTCTAGGTTTCCAAAAACTACCTCCTCGTGGATT CTCCATAGATTGATATGTTCGCTTTTCTATGAATTGAGATGCGAGAACAAAGGAGACATTGGTC GGTGATAAAACTACTTTGTGACTTGGCAGTGCGGCACGACGAAGTAGACGAGAGAATAATTCAT TAACTGTAGGAGCGCTAGGACTAGCTAAAATCTAAACACACTGAATGATGGTAAGTAGGAAATC CAATGCGTGGTCAGATCTTGCTGGAAAAGTCGCACGTTAGGTTTTTGTTGCTGGAGAGTGGGGG ACCCATGGTGGTGTTGGTTTTCTCACATTATTGATAAAAACAGCTGATGATGCAAATCAGCCCC AACAGTCGCCAGAAGTTGATGCACGATGACTTGTTGACTGAGTTTTCTTCCCCGTATTTCTCAC CAATGCTCTACTACCATGTGAAAAATATTGGAGAAGAATATTATTGAATTGTGTATTTACATTA TTATACAAAGACTACTTATAATCATTATTATACAATCCTTCATAAAAAAATAATACAATTCTTT ATCAAGTAGGATTCTATATACTATTCCCATTCTAAGTAGGATTGTATATGCTATTCTTCTTCCT ATCTTATTCTAACACTACCAAAACACCATCAAACACCAAATCTATATCTGGTAAATCAGCCATG AACGCCCATCACCTTCACAGTACATCCGATTCTATGACAGCTGGAAACAACCATTTCTCTGACC AATTCATCTTTTTCTATGACACCCTGATATTACACTCCCTCTAGCCTATCTAACAATCATAGCC TCCCTCAAAGATTAGTTTATCCGGTTGAAATTGTGTCTGATTCGCCCGTTGAAACTCCAGTTTG AGGTGACGGTGATGTTCGAAGTAGCATTGCAGTCAAATTTTCCAGAATTTTCCTGCTTTATTCT TATTGAAAGGGCCAATTTTCTTATTCTTGCTTGTGATGGGGACATGGGGTATGTATCCAGCTTG CAGTCTTCGAAGCAGCGAGATTTTAGTGCGTAAGGTTTGTATAGAATTTAGGAAGACATTTCTT CTGTGATATTTATTTTAGTGTATATTTAATAATTAAATTATTGTGTGGAAGTTCTCAAGAACCT GGAAAAATAGATACCTGATCATTGAAGCATGCCCCATCACGTGGTTGAGGATCCTCAATTATAA AGATATATATAATTAAATTATTGTGTGAAAGTTTCCAAGAACCTGGAAAAAAATAGATAACTGG TCATTGCAGCATGCCACATCACCGGGTTGAGGATCTTCAGTTATATAGATATATAGACATAGAT TCATTGGCTTATGATATACAAAACTTTGACTGTTACGTTGTCCTCATTTTCTTTTATTGGAATA AGCAATCATGATATTATGTTGTCTCCAGGATATGAAGATGCTGCCTTAAAGACACAACGTAGTC TTGCAATCTTAAACTTTGGGCAAAGTGCAATATTCAGCATAGCTCTCTCAGCTGCTATGGTTTT ATGTTCTAATGGGATTATGAATGGTGTCATGACTGTTGGTGACTTGGTAGAACTTTTTCTCTAA TTACCTTAGCTGAGTGATTATTTTTTCTGCAGTGTTAGCCCTCTAATAAGAAATATTACTATTT TTTATAGGTCATGGTAAACGGGCTGCTGTTCCAGCTATCGCTTCCACTGAATTTCCTTGGTAGC GTATATCGTGAGACCATCCAAAGTTTAGTGGACATGAAATCAATGTTTCAGTTACTAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.319633683

Conservation Information
Conserved circRNAs	NA
PMCS	0.319633683

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							40045510-40045456(+)
						
						Potential amino acid sequence
						
							MVFNVFPTILEISMVSGILAYRFGASFAWITSLSVAAYIAFTLSITQWRTKFRKEMNKADNDAS
TRAIDSLINYETVKYFNNEVYETEKYDHFLKRYEDAALKTQRSLAILNFGQSAIFSIALSAAMV
LCSNGIMNGVMTVGDLVMVNGLLFQLSLPLNFLGSVYRETIQSLVDMKSMFQLLESRNRWS*(+
)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	40045510-40045456(+)
Potential amino acid sequence	MVFNVFPTILEISMVSGILAYRFGASFAWITSLSVAAYIAFTLSITQWRTKFRKEMNKADNDAS TRAIDSLINYETVKYFNNEVYETEKYDHFLKRYEDAALKTQRSLAILNFGQSAIFSIALSAAMV LCSNGIMNGVMTVGDLVMVNGLLFQLSLPLNFLGSVYRETIQSLVDMKSMFQLLESRNRWS*(+ )
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zuo et al., 2016

circRNA

Detail information of Solyc09g055350.2_circ_g.3

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